Background/Aims: Roux-en-Y gastric bypass surgery is the most common bariatric surgery worldwide. We have described thiamine deficiency in patients with small intestinal bacterial overgrowth after gastric bypass. We hypothesized that symptoms of thiamine deficiency are common after gastric bypass. The aims of this study were to examine the prevalence of and treatment of symptoms of thiamine deficiency after gastric bypass. Methods: This is a prospective study performed in a large urban, community hospital. Consecutive gastric bypass patients seen from February 1, 2008 to May 1, 2009 are included. Thiamine deficiency in this study included both: consistent clinical symptoms and either (1) low blood thiamine level or (2) resolution of clinical symptoms after receiving thiamine. Results: Of 151 patients, 25 females and 2 males met the criteria for thiamine deficiency (prevalence of 18%). In these 27 patients, 12 had one symptom of thiamine deficiency, while 15 had symptoms consistent with multiple subtypes. Eleven patients reported constipation at 0.33-12 years (mean 4.8) after gastric bypass. Elevated serum folate levels were seen in 6 of 10 tested patients and there was an abnormal glucose-hydrogen breath test in 9 of 10 tested patients, supporting the presence of small intestinal bacterial overgrowth. Frequency of defecation improved after thiamine treatment. Conclusion: Thiamine deficiency resulting from small intestinal bacterial overgrowth should be considered in patients being seen for constipation after gastric bypass surgery.